Pathogens in partially treated waste are a health hazard and public safety threat, officials said.

Fishing, crabbing and shellfishing bans in the New Jersey waters of the harbor will remain in effect, said Larry Ragonese, a Department of Environmetal Protection spokesman.

The New York City Department of Environmental Protection also issued an advisory to residents to avoid contact with the water.

While no target date has been set for repairs at the plant to be completed, DiFrancisci said he expected the facility, which has miles of underground chambers and pipes, to be redesigned to withstand the new reality of storms like Sandy.

"Underneath it would be no different than being in a battleship, making sure the doors are watertight," DiFrancisci said.